# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed # under the Apache License, Version 2.0 (the "License"); you may not use # this file except in compliance with the License. You may obtain a copy # of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless # required by applicable law or agreed to in writing, software distributed # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES # OR CONDITIONS OF ANY KIND, either express or implied. See the License for # the specific language governing permissions and limitations under the License. import logging import os import socket cellxgene_location = os.environ.get("CELLXGENE_LOCATION") cellxgene_data = os.environ.get("CELLXGENE_DATA") cellxgene_args = os.environ.get("CELLXGENE_ARGS", None) gateway_port = int(os.environ.get("GATEWAY_PORT", "5005")) external_host = os.environ.get( "EXTERNAL_HOST", os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"), ) external_protocol = os.environ.get( "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http") ) ip = os.environ.get("GATEWAY_IP", "127.0.0.1") extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS") ttl = os.environ.get("GATEWAY_TTL") enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [ "true", "1", ] enable_annotations = os.environ.get( "GATEWAY_ENABLE_ANNOTATIONS", "" ).lower() in ["true", "1",] enable_backed_mode = os.environ.get( "GATEWAY_ENABLE_BACKED_MODE", "" ).lower() in ["true", "1",] env_vars = { "CELLXGENE_LOCATION": cellxgene_location, "CELLXGENE_DATA": cellxgene_data, } optional_env_vars = { "EXTERNAL_HOST": external_host, "EXTERNAL_PROTOCOL": external_protocol, "GATEWAY_IP": ip, "GATEWAY_PORT": gateway_port, "GATEWAY_EXTRA_SCRIPTS": extra_scripts, "GATEWAY_TTL": ttl, "GATEWAY_ENABLE_UPLOAD": enable_upload, "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations, "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode, "CELLXGENE_ARGS": cellxgene_args, } def validate(): if not all(env_vars.values()): raise ValueError( f""" Please ensure that environment variables are set correctly. The ones with None below are missing and need to be set. {env_vars} Set them at the terminal before running the gateway. An example is: export CELLXGENE_LOCATION=~/anaconda/envs/cellxgene-dev/bin/cellxgene export CELLXGENE_DATA=../cellxgene_data """ ) else: logging.getLogger("cellxgene_gateway").info( f"Got required env: {env_vars}", ) logging.getLogger("cellxgene_gateway").info( f"Got optional env: {optional_env_vars}" )